Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

• Transcriptomic Responses of the Marine Diatom Phaeodactylum tricornutum to High Carbon and Low Nitrogen Stress.

  PMID 41522215 · PMC12789813 · Ecology and evolution · 2026 · 8 claims · 6 setups

  Full-text index only

  Low nitrogen elicits a broader transcriptomic response than high CO2 (4267 vs. 2424 DEGs)

  phaeodactylum bulk qpcr enrichment

• Ontological Discovery Environment: a system for integrating gene-phenotype associations.

  PMID 19733230 · PMC2783409 · Genomics · 2009 · 8 claims · 8 setups

  Full-text index only

  ODE is a web-based system for storing, sharing, retrieving and analyzing phenotype-centered genomic data sets across species and experimental systems

  strains integrated bipartite phish gene differential pairwise

• The identification of a Distinct Astrocyte Subtype that Diminishes in Alzheimer's Disease.

  PMID 38502590 · PMC11567244 · Aging and disease · 2024 · 7 claims · 7 setups

  Has reproduction · 57

  A distinct astrocyte subpopulation marked by low GFAP, AQP4+, and CD63+ expression exists in normal brain and is functionally enriched for Aβ clearance and tau protein binding

  hippocampus prefrontal astrocyte frontal single-nuclei gene cell-cell

• RNAmountAlign: Efficient software for local, global, semiglobal pairwise and multiple RNA sequence/structure alignment.

  PMID 31978147 · PMC6980424 · PloS one · 2020 · 7 claims · 6 setups

  Has reproduction · 71

  RNAmountAlign performs pairwise local, global, and semiglobal (query search) alignment and progressive multiple alignment (global and local) using incremental ensemble mountain height, running in O(n^3) time and O(n^2) space for two sequences of length n

  sequences sets target single secondary pairwise sequence

• Comparative Genomics Provides Insight into the Function of Broad-Host Range Sponge Symbionts.

  PMID 34519538 · PMC8546597 · mBio · 2021 · 8 claims · 8 setups

  Has reproduction · 90

  Eleven new genomes were added to the Tethybacterales order and a novel family (Polydorabacteraceae) was identified

  tsitsikamma tethybacterales putative bin genome 16s multi-locus

• Beyond blacklists: a critical assessment of exclusion set generation strategies and alternative approaches.

  PMID 41826793 · PMC13020910 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 8 setups

  Full-text index only

  Pre-generated Blacklist exclusion sets were difficult to reproduce due to sensitivity to input BAM data, aligner choice, and read length

  hg38 gm12878 gse235167 syo-1 chip-seq rna-seq atac-seq

• In vivo antiviral host transcriptional response to SARS-CoV-2 by viral load, sex, and age.

  PMID 32898168 · PMC7478592 · PLoS biology · 2020 · 8 claims · 8 setups

  Has reproduction · 89

  SARS-CoV-2 infection induces a strong interferon-driven antiviral response in the nasopharynx, with up-regulation of viral sensors, T cell/NK chemokines, and antiviral effectors

  nasopharyngeal airway patient-matched swab shotgun gsea biological

• Identifying cis-regulatory sequences by word profile similarity.

  PMID 19730735 · PMC2731932 · PloS one · 2009 · 8 claims · 8 setups

  Full-text index only

  WPH-finder identifies putative co-regulated CRMs by scanning the genome for sequences with word profiles similar to a known CRM, without explicitly defining binding sites

  stripe pair-rule nrsf-bound eve genome-wide chip-chip chip-seq

• MetaPepticon: automated prediction of anticancer peptides from microbial genomes and metagenomes.

  PMID 41918857 · PMC13034871 · PeerJ · 2026 · 7 claims · 6 setups

  Full-text index only

  MetaPepticon is a modular, end-to-end Snakemake pipeline that predicts ACP candidates directly from raw genomic, metagenomic, transcriptomic, metatranscriptomic reads, assembled contigs, or peptide sequences.

  validated gut representative predicted acp shotgun genome

• MicroRNA profiling of BRCA1/2 mutation-carrying and non-mutation-carrying high-grade serous carcinomas of ovary.

  PMID 19798417 · PMC2749450 · PloS one · 2009 · 7 claims · 7 setups

  Full-text index only

  High grade serous carcinomas with and without BRCA1/2 abnormalities show very similar miRNA expression profiles, with no clear clustering separation by BRCA1/2 status

  high ovarian mir-29a mirna unsupervised significance

• IsoSCM: improved and alternative 3' UTR annotation using multiple change-point inference.

  PMID 25406361 · PMC4274634 · RNA (New York, N.Y.) · 2015 · 8 claims · 6 setups

  Has reproduction · 30

  Existing ab initio assemblers (Cufflinks, Scripture) annotate at most one 3' boundary per terminal exon and therefore cannot assemble coexpressed tandem 3' UTR isoforms.

  mapped simulated rna-seq ict1 computational benchmarking 3'-seq

• A stem and progenitor cell-derived gene expression signature is prognostic for survival in myelofibrosis.

  PMID 41481381 · PMC13155955 · Blood · 2026 · 8 claims · 4 setups

  Full-text index only

  A 24-gene HSPC-derived weighted-sum expression score (MPN24) is prognostic for overall survival in myelofibrosis

  peripheral lin-cd34+ pb-mncs pm-c1 bulk single-cell nanostring

• COSMIC (the Catalogue of Somatic Mutations in Cancer): a resource to investigate acquired mutations in human cancer.

  PMID 19906727 · PMC2808858 · Nucleic acids research · 2010 · 8 claims · 6 setups

  Full-text index only

  COSMIC is the largest public resource for information on somatically acquired mutations in human cancer, freely available without restriction

  cancer tumour manual semi-automated candidate

• Developing a novel immune infiltration-associated mitophagy prediction model for amyotrophic lateral sclerosis using bioinformatics strategies.

  PMID 38601155 · PMC11005030 · Frontiers in immunology · 2024 · 8 claims · 8 setups

  Has reproduction · 71

  Mitophagy-related genes associated with immune infiltration have diagnostic/prognostic significance in ALS

  blood als microarray spearman univariate

• Genomic regions and candidate genes selected during the breeding of rice in Vietnam.

  PMID 35899250 · PMC9309459 · Evolutionary applications · 2022 · 8 claims · 7 setups

  Has reproduction · 75

  XP-CLR and FST scans identify genomic regions with distorted allele frequency/differentiation patterns resulting from differential selective pressures between Vietnamese rice subpopulations

  vietnamese indica subpopulation whole-genome whole-genome xp-clr fst

• Single-Cell Transcriptome Analysis Revealed Heterogeneity and Identified Novel Therapeutic Targets for Breast Cancer Subtypes.

  PMID 37190091 · PMC10137100 · Cells · 2023 · 8 claims · 8 setups

  Has reproduction · 54

  Single-cell transcriptomic analysis of EPCAM+Lin- epithelial cells identified unique gene signatures/markers that distinguish ER+, HER2+, ER+HER2+, and TNBC molecular subtypes

  breast epcam+cd45-cd8a-cd4-cd19-cd3e cancer identified single-cell differential crispr-cas9

• fREDUCE: detection of degenerate regulatory elements using correlation with expression.

  PMID 17941998 · PMC2174516 · BMC bioinformatics · 2007 · 6 claims · 5 setups

  Full-text index only

  fREDUCE is a computational method that detects weak or degenerate binding motifs from gene expression or ChIP-chip data by exhaustive search of degenerate IUPAC oligonucleotides

  saccharomyces cerevisiae hepatocytes chip-chip motif-finding gene

• Performance of mitochondrial DNA mutations detecting early stage cancer.

  PMID 18834532 · PMC2572633 · BMC cancer · 2008 · 8 claims · 6 setups

  Full-text index only

  The Affymetrix MitoChip resequencing array is a high-throughput, higher-resolution alternative to capillary sequencing for detecting mtDNA point mutations and heteroplasmy in clinical specimens.

  matched blood mtdna low-quantity mitochondrial capillary str

• Prioritization of candidate cancer genes--an aid to oncogenomic studies.

  PMID 18710882 · PMC2566894 · Nucleic acids research · 2008 · 8 claims · 8 setups

  Full-text index only

  Computational classifiers using combinations of protein conservation, gene structure, protein domains, protein interactions, and regulatory data can distinguish known cancer genes (CD/CR) from unlabelled human genes

  genes cancer interpro interactome averaged cross-validation domain

• Genotypic analysis of two hypervariable human cytomegalovirus genes.

  PMID 18649324 · PMC2658010 · Journal of medical virology · 2008 · 8 claims · 8 setups

  Full-text index only

  UL146 sequences from 184 samples fall into the same 14 genotypes (G1-G14) previously defined, with no new genotypes found.

  hcmv clinical pcr ul146 pcr nested molecular